How to Build CHD@ZJU

CHD related Articles were retrieved from Pubmed, by entering keywords "coronary heart disease" and constrict the publish date from 2000/1/1 to now (2013/1/23). As a result, totally 115898 articles were found and their abstracts were downloaded for text mining. Since some articles didn't contain abstracts, only 88396 abstracts remained.
The text-mining process to get CHD related genes could be divided in to 5 following steps:

  • 1) Extracting all keywords from abstracts and ignoring those keywords start with numbers. 101402 keywords were extracted.

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  • 2) Input these keywords into Gene library in ArrayTrack and find possible related genes. 4674 genes were then found.

  • 3) Put these 4674 genes again into pubmed abstracts to find related aticles. Only genes which offical name or there keyword description (such as prolactin for gene PRL) could be found in the abstract would be remained. As a result, 1247 genes were remained.

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  • 4) Manually examined on the 1247 genes to validate it was acutally related to CHD. Some genes would be filtered if it represents other meanings (such as gene CAD, Entrez ID:790, carbamoyl-phosphate synthetase 2, is mostly meant coronary arterial disease in articles). 681 genes were then validated with at least one reference.

  • 5) All genes was compared with 1078 CHD genes in RGD database, and 370 genes were overlapped. These 370 genes were labels as "RGD_Supported" and the other 293 genes were labels as "REFERED". All 663 genes had supported references in CHD@ZJU which were examined by step 4.

    • How To contact Us

    Collaboration Information: Prof. Xiaohui Fan (fanxh@zju.edu.cn)

    Website using assistance : Leihong Wu (11019004@zju.edu.cn)




    A Multinomial Ordinal Probit Model with Singular Value Decomposition Method for a Multinomial Trait.
  • Author:"Kwon, Soonil;Goodarzi, Mark O;Taylor, Kent D;Cui, Jinrui;Chen, Y-D Ida;Rotter, Jerome I;Hsueh, Willa;Guo, Xiuqing"

  • Published Year:2012

  • Journal:Journal of probability and statistics

  • Abstract:"We developed a multinomial ordinal probit model with singular value decomposition for testing a large number of single nucleotide polymorphisms SNPs simultaneously for association with multidisease status when sample size is much smaller than the number of SNPs. The validity and performance of the method was evaluated via simulation. We applied the method to our real study sample recruited through the Mexican-American Coronary Artery Disease study. We found 3 genes SORCS1, AMPD1, and PPARalpha to be associated with the development of both IGT and IFG, while 5 genes AMPD2, PRKAA2, C5, TCF7L2, and ITR with the IGT mechanism only and 6 genes CAPN10, IL4, NOS3, CD14, GCG, and SORT1 with the IFG mechanism only. These data suggest that IGT and IFG may indicate different physiological mechanism to prediabetes, via different genetic determinants."

  • 10.1155/2012/419832

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